Question: hisat2 run gave 0% alignment
0
gravatar for vinayjrao
22 months ago by
vinayjrao120
JNCASR, India
vinayjrao120 wrote:

Hi,

I analyzed some RNA-Seq data using the old Tuxedo pipeline (Tophat, Cufflinks and cimmeRbund), but learned that there is an improvisation to the tuxedo protocol, so I ran hisat2, but am constantly getting 0% alignment. Is there anything that I'm doing wrong? I'm posting my command below -

hisat2 -p 8 --dta -x ../../data/ref/hg38 -1 ../../data/fastq/BT474_38_1.fastq -2 ../../data/fastq/BT474_38_2.fastq -S ../../data/hisat/bt474/bt474.sam

This was the command I ran. I would also like to point out that hisat2-build -p 8 -c ../../data/ref/hg38.fa ../../data/ref/hg38 took less than 5 seconds to run. Is that normal?

Thanks.

hisat2 rna-seq alignment • 884 views
ADD COMMENTlink modified 22 months ago by Satyajeet Khare1.4k • written 22 months ago by vinayjrao120
1
gravatar for Satyajeet Khare
22 months ago by
Satyajeet Khare1.4k
Pune, India
Satyajeet Khare1.4k wrote:

Change

hisat2-build -p 8 -c ../../data/ref/hg38.fa ../../data/ref/hg38

to

hisat2-build -p 8 ../../data/ref/hg38.fa ../../data/ref/hg38
ADD COMMENTlink written 22 months ago by Satyajeet Khare1.4k

Thanks a lot, Satya. Could you please explain to me why this works though?

ADD REPLYlink written 22 months ago by vinayjrao120
1

If I am not wrong you will have to provide actual sequence in the cmd line with -c option. According the manual...

-c                      reference sequences given on cmd line (as
                            <reference_in>)
ADD REPLYlink written 22 months ago by Satyajeet Khare1.4k

Oh, OK. Thanks again. I didn't think of that.

ADD REPLYlink written 22 months ago by vinayjrao120
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